diff cpt_intersect_adj/intersect_and_adjacent.xml @ 0:4c72b6accdee draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_intersect_adj/intersect_and_adjacent.xml	Fri May 13 05:05:59 2022 +0000
@@ -0,0 +1,52 @@
+<?xml version="1.0"?>
+<tool id="edu.tamu.cpt.gff3.intersect_and_adjacent" name="Intersect and Adjacent" version="21.0.0">
+  <description>Outputs nearby top-level GFF features from two GFF3 files</description>
+  <macros>
+    <import>macros.xml</import>
+		<import>cpt-macros.xml</import>
+  </macros>
+  <requirements>
+      			<requirement type="package" version="3.7">python</requirement>
+			<requirement type="package" version="1.79">biopython</requirement>
+			<requirement type="package" version="1.1.3">cpt_gffparser</requirement>  
+      <requirement type="package" version="3.0.2">intervaltree</requirement>
+  </requirements>
+  <command detect_errors="aggressive"><![CDATA[
+$__tool_directory__/intersect_and_adjacent.py
+"$gff3_data_a"
+"$gff3_data_b"
+$window
+$stranding
+--oa $oa
+--ob $ob
+]]></command>
+  <inputs>
+    <param label="GFF3 Annotations A" name="gff3_data_a" type="data" format="gff3"/>
+    <param label="GFF3 Annotations B" name="gff3_data_b" type="data" format="gff3"/>
+    <param label="Adjacency Window Size" name="window" type="integer" value = "0"/>
+    <param label="Only allow adjacencies for features on the same strand" name="stranding" type="boolean" checked="false" truevalue="-stranding" falsevalue="" />
+  </inputs>
+  <outputs>
+    <data format="gff3" name="oa" label="GFF3 Annotations from ${gff3_data_a.name} in ${gff3_data_b.name}"/>
+    <data format="gff3" name="ob" label="GFF3 Annotations from ${gff3_data_b.name} in ${gff3_data_a.name}"/>
+  </outputs>
+  <tests>
+		<test>
+			<param name="gff3_data_a" value="T7_IntersectAIn.gff3" />
+			<param name="gff3_data_b" value="T7_IntersectBIn.gff3" />
+                        <param name="window" value= "50" />
+                        <param name="stranding" value= "-stranding"/>
+			<output name="oa" file="T7_IntersectAOut.gff3"/>
+			<output name="ob" file="T7_IntersectBOut.gff3"/>
+		</test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Given two input files, this tool computes the members of A that are within
+"Window" nucleotides of a member of B, and vice versa. It then produces
+two gff3 outputs, one being the features of GFF A that pass this check,
+and the other being the features of GFF B that pass.
+]]></help>
+		<expand macro="citations-2020" />
+</tool>